Helium-3 is a precious noble gas, which is essential in many advanced technologies such as cryogenics, isotope labeling and nuclear weapons. The current imbalance of 3He demand and supply shortage leads to the search for an efficient membrane with high performance for 3He separation. In this study, based on first-principles calculations, we demonstrated that highly efficient 3He harvesting can be achieved in a nanoporous graphenylene membrane with industrially-acceptable selectivity and permeance. The quantum tunneling effect leads to 3He harvesting with high efficiency via kinetic sieving. Both the quantum tunneling effect and zero-point energy (ZPE) determine the 3He/4He separation via thermally-driven equilibrium sieving, where the ZPE effect dominates efficient 3He/4He separation between two reservoirs. The quantum effects revealed in this work suggest that the nanoporous graphenylene membrane is promising for efficient 3He harvesting that can be exploited for industrial applications.